.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH TOPHAT "1" "May 2016" "tophat 2.1.1+dfsg" "User Commands"
.SH NAME
tophat \- TopHat maps short sequences from spliced transcripts to whole genomes
.SH DESCRIPTION
tophat:
TopHat maps short sequences from spliced transcripts to whole genomes.
.SS "Usage:"
.TP
tophat [options] <bowtie_index> <reads1[,reads2,...]> [reads1[,reads2,...]] \e
[quals1,[quals2,...]] [quals1[,quals2,...]]
.SH OPTIONS
.HP
\fB\-v\fR/\-\-version
.TP
\fB\-o\fR/\-\-output\-dir
<string>    [ default: ./tophat_out         ]
.TP
\fB\-\-bowtie1\fR
[ default: bowtie2              ]
.TP
\fB\-N\fR/\-\-read\-mismatches
<int>       [ default: 2                    ]
.TP
\fB\-\-read\-gap\-length\fR
<int>       [ default: 2                    ]
.TP
\fB\-\-read\-edit\-dist\fR
<int>       [ default: 2                    ]
.TP
\fB\-\-read\-realign\-edit\-dist\fR
<int>       [ default: "read\-edit\-dist" + 1 ]
.TP
\fB\-a\fR/\-\-min\-anchor
<int>       [ default: 8                    ]
.TP
\fB\-m\fR/\-\-splice\-mismatches
<0\-2>       [ default: 0                    ]
.TP
\fB\-i\fR/\-\-min\-intron\-length
<int>       [ default: 50                   ]
.TP
\fB\-I\fR/\-\-max\-intron\-length
<int>       [ default: 500000               ]
.TP
\fB\-g\fR/\-\-max\-multihits
<int>       [ default: 20                   ]
.HP
\fB\-\-suppress\-hits\fR
.TP
\fB\-x\fR/\-\-transcriptome\-max\-hits
<int>       [ default: 60                   ]
.TP
\fB\-M\fR/\-\-prefilter\-multihits
( for \fB\-G\fR/\-\-GTF option, enable
an initial bowtie search
against the genome )
.TP
\fB\-\-max\-insertion\-length\fR
<int>       [ default: 3                    ]
.TP
\fB\-\-max\-deletion\-length\fR
<int>       [ default: 3                    ]
.HP
\fB\-\-solexa\-quals\fR
.TP
\fB\-\-solexa1\fR.3\-quals
(same as phred64\-quals)
.TP
\fB\-\-phred64\-quals\fR
(same as solexa1.3\-quals)
.HP
\fB\-Q\fR/\-\-quals
.HP
\fB\-\-integer\-quals\fR
.TP
\fB\-C\fR/\-\-color
(Solid \- color space)
.HP
\fB\-\-color\-out\fR
.TP
\fB\-\-library\-type\fR
<string>    (fr\-unstranded, fr\-firststrand,
fr\-secondstrand)
.TP
\fB\-p\fR/\-\-num\-threads
<int>       [ default: 1                   ]
.TP
\fB\-R\fR/\-\-resume
<out_dir>   ( try to resume execution )
.TP
\fB\-G\fR/\-\-GTF
<filename>  (GTF/GFF with known transcripts)
.TP
\fB\-\-transcriptome\-index\fR
<bwtidx>    (transcriptome bowtie index)
.TP
\fB\-T\fR/\-\-transcriptome\-only
(map only to the transcriptome)
.TP
\fB\-j\fR/\-\-raw\-juncs
<filename>
.TP
\fB\-\-insertions\fR
<filename>
.TP
\fB\-\-deletions\fR
<filename>
.TP
\fB\-r\fR/\-\-mate\-inner\-dist
<int>       [ default: 50                  ]
.TP
\fB\-\-mate\-std\-dev\fR
<int>       [ default: 20                  ]
.HP
\fB\-\-no\-novel\-juncs\fR
.HP
\fB\-\-no\-novel\-indels\fR
.HP
\fB\-\-no\-gtf\-juncs\fR
.HP
\fB\-\-no\-coverage\-search\fR
.HP
\fB\-\-coverage\-search\fR
.HP
\fB\-\-microexon\-search\fR
.HP
\fB\-\-keep\-tmp\fR
.TP
\fB\-\-tmp\-dir\fR
<dirname>   [ default: <output_dir>/tmp ]
.TP
\fB\-z\fR/\-\-zpacker
<program>   [ default: gzip             ]
.TP
\fB\-X\fR/\-\-unmapped\-fifo
[use mkfifo to compress more temporary
files for color space reads]
.SS "Advanced Options:"
.HP
\fB\-\-report\-secondary\-alignments\fR
.HP
\fB\-\-no\-discordant\fR
.HP
\fB\-\-no\-mixed\fR
.TP
\fB\-\-segment\-mismatches\fR
<int>       [ default: 2                ]
.TP
\fB\-\-segment\-length\fR
<int>       [ default: 25               ]
.TP
\fB\-\-bowtie\-n\fR
[ default: bowtie \fB\-v\fR        ]
.TP
\fB\-\-min\-coverage\-intron\fR
<int>       [ default: 50               ]
.TP
\fB\-\-max\-coverage\-intron\fR
<int>       [ default: 20000            ]
.TP
\fB\-\-min\-segment\-intron\fR
<int>       [ default: 50               ]
.TP
\fB\-\-max\-segment\-intron\fR
<int>       [ default: 500000           ]
.TP
\fB\-\-no\-sort\-bam\fR
(Output BAM is not coordinate\-sorted)
.TP
\fB\-\-no\-convert\-bam\fR
(Do not output bam format.
Output is <output_dir>/accepted_hits.sam)
.HP
\fB\-\-keep\-fasta\-order\fR
.HP
\fB\-\-allow\-partial\-mapping\fR
.SS "Bowtie2 related options:"
.IP
Preset options in \fB\-\-end\-to\-end\fR mode (local alignment is not used in TopHat2)
.HP
\fB\-\-b2\-very\-fast\fR
.HP
\fB\-\-b2\-fast\fR
.HP
\fB\-\-b2\-sensitive\fR
.HP
\fB\-\-b2\-very\-sensitive\fR
.IP
Alignment options
.TP
\fB\-\-b2\-N\fR
<int>       [ default: 0                ]
.TP
\fB\-\-b2\-L\fR
<int>       [ default: 20               ]
.TP
\fB\-\-b2\-i\fR
<func>      [ default: S,1,1.25         ]
.TP
\fB\-\-b2\-n\-ceil\fR
<func>      [ default: L,0,0.15         ]
.TP
\fB\-\-b2\-gbar\fR
<int>       [ default: 4                ]
.IP
Scoring options
.TP
\fB\-\-b2\-mp\fR
<int>,<int> [ default: 6,2              ]
.TP
\fB\-\-b2\-np\fR
<int>       [ default: 1                ]
.TP
\fB\-\-b2\-rdg\fR
<int>,<int> [ default: 5,3              ]
.TP
\fB\-\-b2\-rfg\fR
<int>,<int> [ default: 5,3              ]
.TP
\fB\-\-b2\-score\-min\fR
<func>      [ default: L,\-0.6,\-0.6      ]
.IP
Effort options
.TP
\fB\-\-b2\-D\fR
<int>       [ default: 15               ]
.TP
\fB\-\-b2\-R\fR
<int>       [ default: 2                ]
.SS "Fusion related options:"
.HP
\fB\-\-fusion\-search\fR
.TP
\fB\-\-fusion\-anchor\-length\fR
<int>       [ default: 20               ]
.TP
\fB\-\-fusion\-min\-dist\fR
<int>       [ default: 10000000         ]
.TP
\fB\-\-fusion\-read\-mismatches\fR
<int>       [ default: 2                ]
.TP
\fB\-\-fusion\-multireads\fR
<int>       [ default: 2                ]
.TP
\fB\-\-fusion\-multipairs\fR
<int>       [ default: 2                ]
.TP
\fB\-\-fusion\-ignore\-chromosomes\fR
<list>      [ e.g, <chrM,chrX>          ]
.TP
\fB\-\-fusion\-do\-not\-resolve\-conflicts\fR
[this is for test purposes  ]
.SS "SAM Header Options (for embedding sequencing run metadata in output):"
.TP
\fB\-\-rg\-id\fR
<string>    (read group ID)
.TP
\fB\-\-rg\-sample\fR
<string>    (sample ID)
.TP
\fB\-\-rg\-library\fR
<string>    (library ID)
.TP
\fB\-\-rg\-description\fR
<string>    (descriptive string, no tabs allowed)
.TP
\fB\-\-rg\-platform\-unit\fR
<string>    (e.g Illumina lane ID)
.TP
\fB\-\-rg\-center\fR
<string>    (sequencing center name)
.TP
\fB\-\-rg\-date\fR
<string>    (ISO 8601 date of the sequencing run)
.TP
\fB\-\-rg\-platform\fR
<string>    (Sequencing platform descriptor)
.IP
for detailed help see http://ccb.jhu.edu/software/tophat/manual.shtml